devtools::install_github("gledguri/QM",dependencies = TRUE, force = T )
library(QM)
load_QM_packages()Quantitative Metabarcoding
0.1 Load the package and its dependencies
0.2 Load the data
# data(herring_qpcr);force(herring_qpcr)
data(cod_qpcr);force(cod_qpcr)
data(metabarcoding);force(metabarcoding)cod_qpcr Well Sample_name Species Sample_type Ct Plate Std_concentration
1 A1 Std-CH1 Clupea harengus STANDARD 20.67928886 Plate_B 1e+06
2 B1 Std-CH2 Clupea harengus STANDARD 24.28047562 Plate_B 1e+05
3 C1 Std-CH3 Clupea harengus STANDARD 27.46961784 Plate_B 1e+04
4 D1 Std-CH4 Clupea harengus STANDARD 30.63396072 Plate_B 1e+03
5 E1 Std-CH5 Clupea harengus STANDARD 34.198452 Plate_B 1e+02
6 F1 Std-CH6 Clupea harengus STANDARD 36.77652359 Plate_B 1e+01
7 G1 Std-CH7 Clupea harengus STANDARD 39.35696793 Plate_B 1e+00
8 A2 Std-CH1 Clupea harengus STANDARD 20.85572815 Plate_B 1e+06
9 B2 Std-CH2 Clupea harengus STANDARD 24.01898384 Plate_B 1e+05
10 C2 Std-CH3 Clupea harengus STANDARD 27.45393944 Plate_B 1e+04
11 D2 Std-CH4 Clupea harengus STANDARD 30.65498352 Plate_B 1e+03
12 E2 Std-CH5 Clupea harengus STANDARD 33.84698105 Plate_B 1e+02
13 F2 Std-CH6 Clupea harengus STANDARD 36.84316635 Plate_B 1e+01
14 G2 Std-CH7 Clupea harengus STANDARD Undetermined Plate_B 1e+00
15 A3 2021624_10 Clupea harengus UNKNOWN 35.09906387 Plate_B NA
16 B3 2021624_8 Clupea harengus UNKNOWN 37.30815125 Plate_B NA
17 C3 2021624_42 Clupea harengus UNKNOWN Undetermined Plate_B NA
18 D3 2021624_30 Clupea harengus UNKNOWN 39.82544708 Plate_B NA
19 E3 2021624_14 Clupea harengus UNKNOWN Undetermined Plate_B NA
20 F3 2021624_32 Clupea harengus UNKNOWN 38.48879623 Plate_B NA
21 H3 2021624_43 Clupea harengus UNKNOWN 40.76032257 Plate_B NA
22 A4 2021624_10 Clupea harengus UNKNOWN 35.12607574 Plate_B NA
23 B4 2021624_8 Clupea harengus UNKNOWN 37.36190033 Plate_B NA
24 C4 2021624_42 Clupea harengus UNKNOWN Undetermined Plate_B NA
25 D4 2021624_30 Clupea harengus UNKNOWN Undetermined Plate_B NA
26 E4 2021624_14 Clupea harengus UNKNOWN Undetermined Plate_B NA
27 F4 2021624_32 Clupea harengus UNKNOWN 37.62449646 Plate_B NA
28 H4 2021624_43 Clupea harengus UNKNOWN 39.57535172 Plate_B NA
29 A5 2021624_18 Clupea harengus UNKNOWN 37.13931656 Plate_B NA
30 B5 2021624_40 Clupea harengus UNKNOWN Undetermined Plate_B NA
31 C5 2021624_25 Clupea harengus UNKNOWN Undetermined Plate_B NA
32 D5 2021624_22 Clupea harengus UNKNOWN 38.31303406 Plate_B NA
33 E5 2021624_15 Clupea harengus UNKNOWN 36.2652626 Plate_B NA
34 F5 2021624_44 Clupea harengus UNKNOWN 45.76896667 Plate_B NA
35 G5 2021624_5 Clupea harengus UNKNOWN 36.17409515 Plate_B NA
36 H5 2021624_16 Clupea harengus UNKNOWN Undetermined Plate_B NA
37 A6 2021624_18 Clupea harengus UNKNOWN 37.69597244 Plate_B NA
38 B6 2021624_40 Clupea harengus UNKNOWN Undetermined Plate_B NA
39 C6 2021624_25 Clupea harengus UNKNOWN 41.2206459 Plate_B NA
40 D6 2021624_22 Clupea harengus UNKNOWN 39.17343903 Plate_B NA
41 E6 2021624_15 Clupea harengus UNKNOWN 37.38412094 Plate_B NA
42 F6 2021624_44 Clupea harengus UNKNOWN 42.63734436 Plate_B NA
43 G6 2021624_5 Clupea harengus UNKNOWN 36.24113846 Plate_B NA
44 H6 2021624_16 Clupea harengus UNKNOWN 39.2844696 Plate_B NA
45 A7 2021624_27 Clupea harengus UNKNOWN 39.76254654 Plate_B NA
46 B7 2021624_4 Clupea harengus UNKNOWN 41.51676178 Plate_B NA
47 C7 2021624_11 Clupea harengus UNKNOWN 35.69413757 Plate_B NA
48 D7 2021624_26 Clupea harengus UNKNOWN 37.39764404 Plate_B NA
49 E7 2021624_41 Clupea harengus UNKNOWN 38.89216232 Plate_B NA
50 F7 2021624_29 Clupea harengus UNKNOWN 40.97231674 Plate_B NA
51 H7 2021624_6 Clupea harengus UNKNOWN 37.86229324 Plate_B NA
52 A8 2021624_27 Clupea harengus UNKNOWN Undetermined Plate_B NA
53 B8 2021624_4 Clupea harengus UNKNOWN 35.72262573 Plate_B NA
54 C8 2021624_11 Clupea harengus UNKNOWN 35.77841949 Plate_B NA
55 D8 2021624_26 Clupea harengus UNKNOWN 39.48923874 Plate_B NA
56 E8 2021624_41 Clupea harengus UNKNOWN 37.65555954 Plate_B NA
57 F8 2021624_29 Clupea harengus UNKNOWN Undetermined Plate_B NA
58 H8 2021624_6 Clupea harengus UNKNOWN 39.03905869 Plate_B NA
59 A9 2021624_33 Clupea harengus UNKNOWN 39.78116608 Plate_B NA
60 B9 2021624_17 Clupea harengus UNKNOWN Undetermined Plate_B NA
61 C9 2021624_28 Clupea harengus UNKNOWN 43.33337021 Plate_B NA
62 D9 2021624_38 Clupea harengus UNKNOWN 46.12921524 Plate_B NA
63 E9 2021624_3 Clupea harengus UNKNOWN 37.4945755 Plate_B NA
64 F9 2021624_20 Clupea harengus UNKNOWN Undetermined Plate_B NA
65 G9 2021624_19 Clupea harengus UNKNOWN 41.06113434 Plate_B NA
66 H9 2021624_36 Clupea harengus UNKNOWN 40.08838272 Plate_B NA
67 A10 2021624_33 Clupea harengus UNKNOWN 39.83427429 Plate_B NA
68 B10 2021624_17 Clupea harengus UNKNOWN Undetermined Plate_B NA
69 C10 2021624_28 Clupea harengus UNKNOWN Undetermined Plate_B NA
70 D10 2021624_38 Clupea harengus UNKNOWN 39.83372116 Plate_B NA
71 E10 2021624_3 Clupea harengus UNKNOWN 36.97294617 Plate_B NA
72 F10 2021624_20 Clupea harengus UNKNOWN Undetermined Plate_B NA
73 G10 2021624_19 Clupea harengus UNKNOWN 34.90359116 Plate_B NA
74 H10 2021624_36 Clupea harengus UNKNOWN 40.28865051 Plate_B NA
75 A11 2021624_21 Clupea harengus UNKNOWN 35.65264893 Plate_B NA
76 B11 2021624_31 Clupea harengus UNKNOWN 39.55165863 Plate_B NA
77 D11 2021624_9 Clupea harengus UNKNOWN 37.7012825 Plate_B NA
78 E11 2021624_39 Clupea harengus UNKNOWN 40.05196381 Plate_B NA
79 G11 2021624_7 Clupea harengus UNKNOWN 36.73715591 Plate_B NA
80 A12 2021624_21 Clupea harengus UNKNOWN 37.03312302 Plate_B NA
81 B12 2021624_31 Clupea harengus UNKNOWN Undetermined Plate_B NA
82 D12 2021624_9 Clupea harengus UNKNOWN 38.43218613 Plate_B NA
83 E12 2021624_39 Clupea harengus UNKNOWN Undetermined Plate_B NA
84 G12 2021624_7 Clupea harengus UNKNOWN 36.23777771 Plate_B NA
85 A1 Std-CH1 Clupea harengus STANDARD 20.89475441 Plate_D 1e+06
86 B1 Std-CH3 Clupea harengus STANDARD 27.75590706 Plate_D 1e+04
87 C1 Std-CH4 Clupea harengus STANDARD 30.63160706 Plate_D 1e+03
88 D1 Std-CH5 Clupea harengus STANDARD 34.11185837 Plate_D 1e+02
89 E1 Std-CH6 Clupea harengus STANDARD 37.31342697 Plate_D 1e+01
90 F1 Std-CH7 Clupea harengus STANDARD 38.6644249 Plate_D 1e+00
91 G1 Std-CH8 Clupea harengus STANDARD 39.65521622 Plate_D 1e-01
92 A2 Std-CH1 Clupea harengus STANDARD 21.04283905 Plate_D 1e+06
93 B2 Std-CH3 Clupea harengus STANDARD 27.64603615 Plate_D 1e+04
94 C2 Std-CH4 Clupea harengus STANDARD 30.80105972 Plate_D 1e+03
95 D2 Std-CH5 Clupea harengus STANDARD 34.07408905 Plate_D 1e+02
96 E2 Std-CH6 Clupea harengus STANDARD 38.12646866 Plate_D 1e+01
97 F2 Std-CH7 Clupea harengus STANDARD 40.2918129 Plate_D 1e+00
98 G2 Std-CH8 Clupea harengus STANDARD 39.65754318 Plate_D 1e-01
99 A3 2021624_37 Clupea harengus UNKNOWN Undetermined Plate_D NA
100 C3 2020620_29 Clupea harengus UNKNOWN Undetermined Plate_D NA
101 D3 2020620_32 Clupea harengus UNKNOWN Undetermined Plate_D NA
102 E3 2020620_16 Clupea harengus UNKNOWN Undetermined Plate_D NA
103 F3 2020620_03 Clupea harengus UNKNOWN 38.66085434 Plate_D NA
104 G3 2020620_12 Clupea harengus UNKNOWN Undetermined Plate_D NA
105 H3 2020620_07 Clupea harengus UNKNOWN Undetermined Plate_D NA
106 A4 2021624_37 Clupea harengus UNKNOWN Undetermined Plate_D NA
107 C4 2020620_29 Clupea harengus UNKNOWN Undetermined Plate_D NA
108 D4 2020620_32 Clupea harengus UNKNOWN Undetermined Plate_D NA
109 E4 2020620_16 Clupea harengus UNKNOWN Undetermined Plate_D NA
110 F4 2020620_03 Clupea harengus UNKNOWN 40.42780304 Plate_D NA
111 G4 2020620_12 Clupea harengus UNKNOWN Undetermined Plate_D NA
112 H4 2020620_07 Clupea harengus UNKNOWN 40.07585526 Plate_D NA
113 A5 2020620_31 Clupea harengus UNKNOWN Undetermined Plate_D NA
114 C5 2020620_28 Clupea harengus UNKNOWN Undetermined Plate_D NA
115 E5 2020620_23 Clupea harengus UNKNOWN Undetermined Plate_D NA
116 F5 2020620_22 Clupea harengus UNKNOWN Undetermined Plate_D NA
117 G5 2020620_19 Clupea harengus UNKNOWN 40.61782074 Plate_D NA
118 H5 2020620_11 Clupea harengus UNKNOWN 40.87185287 Plate_D NA
119 A6 2020620_31 Clupea harengus UNKNOWN Undetermined Plate_D NA
120 C6 2020620_28 Clupea harengus UNKNOWN Undetermined Plate_D NA
121 E6 2020620_23 Clupea harengus UNKNOWN Undetermined Plate_D NA
122 F6 2020620_22 Clupea harengus UNKNOWN Undetermined Plate_D NA
123 G6 2020620_19 Clupea harengus UNKNOWN Undetermined Plate_D NA
124 H6 2020620_11 Clupea harengus UNKNOWN 41.73017502 Plate_D NA
125 A7 2020620_15 Clupea harengus UNKNOWN Undetermined Plate_D NA
126 B7 2020620_30 Clupea harengus UNKNOWN Undetermined Plate_D NA
127 C7 2020620_27 Clupea harengus UNKNOWN 40.10155106 Plate_D NA
128 E7 2020620_20 Clupea harengus UNKNOWN Undetermined Plate_D NA
129 F7 2020620_13 Clupea harengus UNKNOWN Undetermined Plate_D NA
130 G7 2020620_04 Clupea harengus UNKNOWN Undetermined Plate_D NA
131 H7 2020620_21 Clupea harengus UNKNOWN Undetermined Plate_D NA
132 A8 2020620_15 Clupea harengus UNKNOWN Undetermined Plate_D NA
133 B8 2020620_30 Clupea harengus UNKNOWN Undetermined Plate_D NA
134 C8 2020620_27 Clupea harengus UNKNOWN Undetermined Plate_D NA
135 E8 2020620_20 Clupea harengus UNKNOWN 40.43481827 Plate_D NA
136 F8 2020620_13 Clupea harengus UNKNOWN 40.30215454 Plate_D NA
137 G8 2020620_04 Clupea harengus UNKNOWN 39.51931763 Plate_D NA
138 H8 2020620_21 Clupea harengus UNKNOWN Undetermined Plate_D NA
139 A9 2020620_06 Clupea harengus UNKNOWN 38.23839951 Plate_D NA
140 B9 2020620_05 Clupea harengus UNKNOWN 40.26202011 Plate_D NA
141 D9 2020620_14 Clupea harengus UNKNOWN Undetermined Plate_D NA
142 E9 2020620_08 Clupea harengus UNKNOWN Undetermined Plate_D NA
143 F9 2020620_24 Clupea harengus UNKNOWN Undetermined Plate_D NA
144 G9 2019629_16 Clupea harengus UNKNOWN 39.65792084 Plate_D NA
145 H9 2019629_22 Clupea harengus UNKNOWN Undetermined Plate_D NA
146 A10 2020620_06 Clupea harengus UNKNOWN 37.93161774 Plate_D NA
147 B10 2020620_05 Clupea harengus UNKNOWN 39.57629776 Plate_D NA
148 D10 2020620_14 Clupea harengus UNKNOWN Undetermined Plate_D NA
149 E10 2020620_08 Clupea harengus UNKNOWN Undetermined Plate_D NA
150 F10 2020620_24 Clupea harengus UNKNOWN Undetermined Plate_D NA
151 G10 2019629_16 Clupea harengus UNKNOWN 40.47380829 Plate_D NA
152 H10 2019629_22 Clupea harengus UNKNOWN Undetermined Plate_D NA
153 A11 2019629_7 Clupea harengus UNKNOWN Undetermined Plate_D NA
154 B11 2019629_11 Clupea harengus UNKNOWN Undetermined Plate_D NA
155 C11 2019629_15 Clupea harengus UNKNOWN Undetermined Plate_D NA
156 D11 2019629_6 Clupea harengus UNKNOWN 40.02921677 Plate_D NA
157 E11 2019629_31 Clupea harengus UNKNOWN Undetermined Plate_D NA
158 G11 2019629_32 Clupea harengus UNKNOWN 39.20246887 Plate_D NA
159 A12 2019629_7 Clupea harengus UNKNOWN 39.85317612 Plate_D NA
160 B12 2019629_11 Clupea harengus UNKNOWN 40.6131897 Plate_D NA
161 C12 2019629_15 Clupea harengus UNKNOWN Undetermined Plate_D NA
162 D12 2019629_6 Clupea harengus UNKNOWN 39.5435524 Plate_D NA
163 E12 2019629_31 Clupea harengus UNKNOWN Undetermined Plate_D NA
164 G12 2019629_32 Clupea harengus UNKNOWN 39.79040527 Plate_D NA
165 A1 Std-CH1 Clupea harengus STANDARD 21.07470703 Plate_E 1e+06
166 B1 Std-CH3 Clupea harengus STANDARD 27.61070824 Plate_E 1e+04
167 C1 Std-CH4 Clupea harengus STANDARD 30.86172676 Plate_E 1e+03
168 D1 Std-CH5 Clupea harengus STANDARD 34.17502975 Plate_E 1e+02
169 E1 Std-CH6 Clupea harengus STANDARD 38.08354187 Plate_E 1e+01
170 F1 Std-CH7 Clupea harengus STANDARD Undetermined Plate_E 1e+00
171 G1 Std-CH8 Clupea harengus STANDARD 44.88344574 Plate_E 1e-01
172 A2 Std-CH1 Clupea harengus STANDARD 20.8622818 Plate_E 1e+06
173 B2 Std-CH3 Clupea harengus STANDARD 27.53244209 Plate_E 1e+04
174 C2 Std-CH4 Clupea harengus STANDARD 30.87360191 Plate_E 1e+03
175 D2 Std-CH5 Clupea harengus STANDARD 34.01688004 Plate_E 1e+02
176 E2 Std-CH6 Clupea harengus STANDARD 38.36595154 Plate_E 1e+01
177 F2 Std-CH7 Clupea harengus STANDARD Undetermined Plate_E 1e+00
178 G2 Std-CH8 Clupea harengus STANDARD Undetermined Plate_E 1e-01
179 A3 2019629_28 Clupea harengus UNKNOWN Undetermined Plate_E NA
180 D3 2019629_4 Clupea harengus UNKNOWN Undetermined Plate_E NA
181 E3 2019629_12 Clupea harengus UNKNOWN Undetermined Plate_E NA
182 F3 2019629_29 Clupea harengus UNKNOWN 40.07517242 Plate_E NA
183 G3 2019629_21 Clupea harengus UNKNOWN Undetermined Plate_E NA
184 A4 2019629_28 Clupea harengus UNKNOWN Undetermined Plate_E NA
185 D4 2019629_4 Clupea harengus UNKNOWN Undetermined Plate_E NA
186 E4 2019629_12 Clupea harengus UNKNOWN Undetermined Plate_E NA
187 F4 2019629_29 Clupea harengus UNKNOWN Undetermined Plate_E NA
188 G4 2019629_21 Clupea harengus UNKNOWN Undetermined Plate_E NA
189 A5 2019629_28 Clupea harengus UNKNOWN Undetermined Plate_E NA
190 D5 2019629_4 Clupea harengus UNKNOWN Undetermined Plate_E NA
191 E5 2019629_12 Clupea harengus UNKNOWN 40.28800583 Plate_E NA
192 F5 2019629_29 Clupea harengus UNKNOWN 40.9784584 Plate_E NA
193 G5 2019629_21 Clupea harengus UNKNOWN Undetermined Plate_E NA
194 A6 2019629_28 Clupea harengus UNKNOWN Undetermined Plate_E NA
195 D6 2019629_4 Clupea harengus UNKNOWN Undetermined Plate_E NA
196 E6 2019629_22 Clupea harengus UNKNOWN 39.99228668 Plate_E NA
197 F6 2019629_29 Clupea harengus UNKNOWN 40.9406395 Plate_E NA
198 G6 2019629_21 Clupea harengus UNKNOWN Undetermined Plate_E NA
199 A7 2019629_14 Clupea harengus UNKNOWN Undetermined Plate_E NA
200 B7 2019629_23 Clupea harengus UNKNOWN Undetermined Plate_E NA
201 C7 2019629_8 Clupea harengus UNKNOWN 40.81485748 Plate_E NA
202 D7 2019629_20 Clupea harengus UNKNOWN Undetermined Plate_E NA
203 E7 2019629_24 Clupea harengus UNKNOWN Undetermined Plate_E NA
204 F7 2019629_19 Clupea harengus UNKNOWN Undetermined Plate_E NA
205 G7 2019629_5 Clupea harengus UNKNOWN Undetermined Plate_E NA
206 H7 2019629_3 Clupea harengus UNKNOWN Undetermined Plate_E NA
207 A8 2019629_14 Clupea harengus UNKNOWN Undetermined Plate_E NA
208 B8 2019629_23 Clupea harengus UNKNOWN 39.60705566 Plate_E NA
209 C8 2019629_8 Clupea harengus UNKNOWN Undetermined Plate_E NA
210 D8 2019629_20 Clupea harengus UNKNOWN Undetermined Plate_E NA
211 E8 2019629_24 Clupea harengus UNKNOWN Undetermined Plate_E NA
212 F8 2019629_19 Clupea harengus UNKNOWN Undetermined Plate_E NA
213 G8 2019629_5 Clupea harengus UNKNOWN Undetermined Plate_E NA
214 H8 2019629_3 Clupea harengus UNKNOWN Undetermined Plate_E NA
215 A9 2019629_14 Clupea harengus UNKNOWN Undetermined Plate_E NA
216 B9 2019629_23 Clupea harengus UNKNOWN 39.78777313 Plate_E NA
217 C9 2019629_8 Clupea harengus UNKNOWN 40.69521713 Plate_E NA
218 D9 2019629_20 Clupea harengus UNKNOWN Undetermined Plate_E NA
219 E9 2019629_24 Clupea harengus UNKNOWN Undetermined Plate_E NA
220 F9 2019629_19 Clupea harengus UNKNOWN 42.15032959 Plate_E NA
221 G9 2019629_5 Clupea harengus UNKNOWN Undetermined Plate_E NA
222 H9 2019629_3 Clupea harengus UNKNOWN Undetermined Plate_E NA
223 A10 2019629_14 Clupea harengus UNKNOWN Undetermined Plate_E NA
224 B10 2019629_22 Clupea harengus UNKNOWN 45.96703339 Plate_E NA
225 C10 2019629_8 Clupea harengus UNKNOWN Undetermined Plate_E NA
226 D10 2019629_7 Clupea harengus UNKNOWN Undetermined Plate_E NA
227 E10 2019629_7 Clupea harengus UNKNOWN Undetermined Plate_E NA
228 F10 2019629_11 Clupea harengus UNKNOWN Undetermined Plate_E NA
229 G10 2019629_5 Clupea harengus UNKNOWN Undetermined Plate_E NA
230 H10 2019629_3 Clupea harengus UNKNOWN 40.49952316 Plate_E NA
231 A11 2019629_27 Clupea harengus UNKNOWN Undetermined Plate_E NA
232 B11 2019629_27 Clupea harengus UNKNOWN Undetermined Plate_E NA
233 C11 2019629_13 Clupea harengus UNKNOWN 38.52088928 Plate_E NA
234 D11 2019629_13 Clupea harengus UNKNOWN 39.43684387 Plate_E NA
235 E11 2019629_30 Clupea harengus UNKNOWN Undetermined Plate_E NA
236 F11 2019629_30 Clupea harengus UNKNOWN Undetermined Plate_E NA
237 G11 2019629_32 Clupea harengus UNKNOWN 39.62968826 Plate_E NA
238 A12 2019629_27 Clupea harengus UNKNOWN Undetermined Plate_E NA
239 B12 2019629_11 Clupea harengus UNKNOWN 40.35699081 Plate_E NA
240 C12 2019629_13 Clupea harengus UNKNOWN 38.6665802 Plate_E NA
241 D12 2019629_15 Clupea harengus UNKNOWN Undetermined Plate_E NA
242 E12 2019629_30 Clupea harengus UNKNOWN Undetermined Plate_E NA
243 F12 2019629_15 Clupea harengus UNKNOWN 42.94013977 Plate_E NA
244 G12 2019629_32 Clupea harengus UNKNOWN 38.93134689 Plate_E NA
245 A1 Std-CH1 Clupea harengus STANDARD 21.23091507 Plate_F 1e+06
246 B1 Std-CH3 Clupea harengus STANDARD 27.66345215 Plate_F 1e+04
247 C1 Std-CH4 Clupea harengus STANDARD 31.19370461 Plate_F 1e+03
248 D1 Std-CH5 Clupea harengus STANDARD 34.4101181 Plate_F 1e+02
249 E1 Std-CH6 Clupea harengus STANDARD 37.87618256 Plate_F 1e+01
250 F1 Std-CH7 Clupea harengus STANDARD 39.54518127 Plate_F 1e+00
251 G1 Std-CH8 Clupea harengus STANDARD 40.39379883 Plate_F 1e-01
252 A2 Std-CH1 Clupea harengus STANDARD 21.11040688 Plate_F 1e+06
253 B2 Std-CH3 Clupea harengus STANDARD 27.6223526 Plate_F 1e+04
254 C2 Std-CH4 Clupea harengus STANDARD 31.78951645 Plate_F 1e+03
255 E2 Std-CH6 Clupea harengus STANDARD 37.73504639 Plate_F 1e+01
256 F2 Std-CH7 Clupea harengus STANDARD 39.50231171 Plate_F 1e+00
257 G2 Std-CH8 Clupea harengus STANDARD Undetermined Plate_F 1e-01
258 B3 2021624_7 Clupea harengus UNKNOWN 34.95716476 Plate_F NA
259 C3 2021624_37 Clupea harengus UNKNOWN Undetermined Plate_F NA
260 F3 2020620_29 Clupea harengus UNKNOWN Undetermined Plate_F NA
261 G3 2020620_32 Clupea harengus UNKNOWN 39.50717545 Plate_F NA
262 H3 2020620_16 Clupea harengus UNKNOWN Undetermined Plate_F NA
263 B4 2021624_7 Clupea harengus UNKNOWN 35.16669846 Plate_F NA
264 C4 2021624_37 Clupea harengus UNKNOWN Undetermined Plate_F NA
265 F4 2020620_29 Clupea harengus UNKNOWN Undetermined Plate_F NA
266 G4 2020620_32 Clupea harengus UNKNOWN 39.05901337 Plate_F NA
267 H4 2020620_16 Clupea harengus UNKNOWN Undetermined Plate_F NA
268 A5 2020620_03 Clupea harengus UNKNOWN 38.81376648 Plate_F NA
269 B5 2020620_12 Clupea harengus UNKNOWN Undetermined Plate_F NA
270 C5 2020620_07 Clupea harengus UNKNOWN 39.77295685 Plate_F NA
271 D5 2020620_31 Clupea harengus UNKNOWN Undetermined Plate_F NA
272 F5 2020620_28 Clupea harengus UNKNOWN Undetermined Plate_F NA
273 H5 2020620_23 Clupea harengus UNKNOWN Undetermined Plate_F NA
274 A6 2020620_03 Clupea harengus UNKNOWN Undetermined Plate_F NA
275 B6 2020620_12 Clupea harengus UNKNOWN Undetermined Plate_F NA
276 C6 2020620_07 Clupea harengus UNKNOWN 40.1975174 Plate_F NA
277 D6 2020620_31 Clupea harengus UNKNOWN Undetermined Plate_F NA
278 F6 2020620_28 Clupea harengus UNKNOWN Undetermined Plate_F NA
279 H6 2020620_23 Clupea harengus UNKNOWN 40.87150955 Plate_F NA
280 A7 2020620_22 Clupea harengus UNKNOWN Undetermined Plate_F NA
281 B7 2020620_19 Clupea harengus UNKNOWN Undetermined Plate_F NA
282 C7 2020620_11 Clupea harengus UNKNOWN Undetermined Plate_F NA
283 D7 2020620_15 Clupea harengus UNKNOWN Undetermined Plate_F NA
284 E7 2020620_30 Clupea harengus UNKNOWN Undetermined Plate_F NA
285 F7 2020620_27 Clupea harengus UNKNOWN 40.62250519 Plate_F NA
286 H7 2020620_20 Clupea harengus UNKNOWN Undetermined Plate_F NA
287 A8 2020620_22 Clupea harengus UNKNOWN Undetermined Plate_F NA
288 B8 2020620_19 Clupea harengus UNKNOWN Undetermined Plate_F NA
289 C8 2020620_11 Clupea harengus UNKNOWN Undetermined Plate_F NA
290 D8 2020620_15 Clupea harengus UNKNOWN Undetermined Plate_F NA
291 E8 2020620_30 Clupea harengus UNKNOWN Undetermined Plate_F NA
292 F8 2020620_27 Clupea harengus UNKNOWN Undetermined Plate_F NA
293 H8 2020620_20 Clupea harengus UNKNOWN Undetermined Plate_F NA
294 A9 2020620_13 Clupea harengus UNKNOWN Undetermined Plate_F NA
295 B9 2020620_04 Clupea harengus UNKNOWN 39.4901123 Plate_F NA
296 C9 2020620_21 Clupea harengus UNKNOWN Undetermined Plate_F NA
297 D9 2020620_06 Clupea harengus UNKNOWN 39.3844986 Plate_F NA
298 E9 2020620_05 Clupea harengus UNKNOWN Undetermined Plate_F NA
299 G9 2020620_14 Clupea harengus UNKNOWN 40.98209763 Plate_F NA
300 H9 2020620_08 Clupea harengus UNKNOWN Undetermined Plate_F NA
301 A10 2020620_13 Clupea harengus UNKNOWN Undetermined Plate_F NA
302 B10 2020620_04 Clupea harengus UNKNOWN Undetermined Plate_F NA
303 C10 2020620_21 Clupea harengus UNKNOWN Undetermined Plate_F NA
304 D10 2020620_06 Clupea harengus UNKNOWN 38.73543549 Plate_F NA
305 E10 2020620_05 Clupea harengus UNKNOWN 40.19083786 Plate_F NA
306 G10 2020620_14 Clupea harengus UNKNOWN Undetermined Plate_F NA
307 H10 2020620_08 Clupea harengus UNKNOWN Undetermined Plate_F NA
308 A11 2020620_24 Clupea harengus UNKNOWN 39.64798737 Plate_F NA
309 C11 2019629_16 Clupea harengus UNKNOWN 39.21881485 Plate_F NA
310 D11 2019629_6 Clupea harengus UNKNOWN 39.18229294 Plate_F NA
311 E11 2019629_31 Clupea harengus UNKNOWN Undetermined Plate_F NA
312 G11 Std-CH2 Clupea harengus STANDARD 24.00854683 Plate_F 1e+05
313 A12 2020620_24 Clupea harengus UNKNOWN Undetermined Plate_F NA
314 C12 2019629_16 Clupea harengus UNKNOWN 39.65681458 Plate_F NA
315 D12 2019629_6 Clupea harengus UNKNOWN 38.50286484 Plate_F NA
316 E12 2019629_31 Clupea harengus UNKNOWN 39.46422195 Plate_F NA
317 G12 Std-CH2 Clupea harengus STANDARD 24.46125603 Plate_F 1e+05
318 A1 Std-CH1 Clupea harengus STANDARD 20.8891716 Plate_G 1e+06
319 B1 Std-CH3 Clupea harengus STANDARD 27.59408188 Plate_G 1e+04
320 C1 Std-CH4 Clupea harengus STANDARD 30.84783363 Plate_G 1e+03
321 D1 Std-CH5 Clupea harengus STANDARD 33.88689423 Plate_G 1e+02
322 E1 Std-CH6 Clupea harengus STANDARD 37.4319191 Plate_G 1e+01
323 F1 Std-CH7 Clupea harengus STANDARD 40.76457977 Plate_G 1e+00
324 G1 Std-CH8 Clupea harengus STANDARD Undetermined Plate_G 1e-01
325 A2 Std-CH1 Clupea harengus STANDARD 20.89135551 Plate_G 1e+06
326 B2 Std-CH3 Clupea harengus STANDARD 27.26293373 Plate_G 1e+04
327 C2 Std-CH4 Clupea harengus STANDARD 30.70213699 Plate_G 1e+03
328 D2 Std-CH5 Clupea harengus STANDARD 33.9912262 Plate_G 1e+02
329 E2 Std-CH6 Clupea harengus STANDARD 37.77001572 Plate_G 1e+01
330 F2 Std-CH7 Clupea harengus STANDARD Undetermined Plate_G 1e+00
331 G2 Std-CH8 Clupea harengus STANDARD Undetermined Plate_G 1e-01
332 A3 2021624_10 Clupea harengus UNKNOWN 36.4125824 Plate_G NA
333 B3 2021624_8 Clupea harengus UNKNOWN 36.8061676 Plate_G NA
334 C3 2021624_42 Clupea harengus UNKNOWN 41.33824921 Plate_G NA
335 D3 2021624_30 Clupea harengus UNKNOWN Undetermined Plate_G NA
336 E3 2021624_14 Clupea harengus UNKNOWN Undetermined Plate_G NA
337 F3 2021624_32 Clupea harengus UNKNOWN 38.21615219 Plate_G NA
338 H3 2021624_43 Clupea harengus UNKNOWN Undetermined Plate_G NA
339 A4 2021624_10 Clupea harengus UNKNOWN 42.56510544 Plate_G NA
340 B4 2021624_8 Clupea harengus UNKNOWN 37.29789734 Plate_G NA
341 C4 2021624_42 Clupea harengus UNKNOWN 41.87237549 Plate_G NA
342 D4 2021624_30 Clupea harengus UNKNOWN Undetermined Plate_G NA
343 E4 2021624_14 Clupea harengus UNKNOWN Undetermined Plate_G NA
344 F4 2021624_32 Clupea harengus UNKNOWN 38.64439011 Plate_G NA
345 H4 2021624_43 Clupea harengus UNKNOWN 41.30338287 Plate_G NA
346 A5 2021624_18 Clupea harengus UNKNOWN 36.34432983 Plate_G NA
347 B5 2021624_40 Clupea harengus UNKNOWN 40.30106735 Plate_G NA
348 C5 2021624_25 Clupea harengus UNKNOWN Undetermined Plate_G NA
349 D5 2021624_22 Clupea harengus UNKNOWN 39.94377136 Plate_G NA
350 E5 2021624_15 Clupea harengus UNKNOWN 36.63824081 Plate_G NA
351 F5 2021624_44 Clupea harengus UNKNOWN Undetermined Plate_G NA
352 G5 2021624_5 Clupea harengus UNKNOWN 35.89820862 Plate_G NA
353 H5 2021624_16 Clupea harengus UNKNOWN 39.48892212 Plate_G NA
354 A6 2021624_18 Clupea harengus UNKNOWN 36.157547 Plate_G NA
355 B6 2021624_40 Clupea harengus UNKNOWN 38.20215607 Plate_G NA
356 C6 2021624_25 Clupea harengus UNKNOWN Undetermined Plate_G NA
357 D6 2021624_22 Clupea harengus UNKNOWN 40.01337814 Plate_G NA
358 E6 2021624_15 Clupea harengus UNKNOWN 36.47186279 Plate_G NA
359 F6 2021624_44 Clupea harengus UNKNOWN 39.98491669 Plate_G NA
360 G6 2021624_5 Clupea harengus UNKNOWN 37.07023621 Plate_G NA
361 H6 2021624_16 Clupea harengus UNKNOWN 39.49610901 Plate_G NA
362 A7 2021624_27 Clupea harengus UNKNOWN 40.63593674 Plate_G NA
363 B7 2021624_4 Clupea harengus UNKNOWN 36.51871109 Plate_G NA
364 C7 2021624_11 Clupea harengus UNKNOWN 36.05905151 Plate_G NA
365 D7 2021624_26 Clupea harengus UNKNOWN 38.13557053 Plate_G NA
366 E7 2021624_41 Clupea harengus UNKNOWN 40.01876831 Plate_G NA
367 F7 2021624_29 Clupea harengus UNKNOWN 38.95786285 Plate_G NA
368 H7 2021624_6 Clupea harengus UNKNOWN 38.33583069 Plate_G NA
369 A8 2021624_27 Clupea harengus UNKNOWN 41.39300537 Plate_G NA
370 B8 2021624_4 Clupea harengus UNKNOWN 34.62062454 Plate_G NA
371 C8 2021624_11 Clupea harengus UNKNOWN 35.67477417 Plate_G NA
372 D8 2021624_26 Clupea harengus UNKNOWN 38.78547668 Plate_G NA
373 E8 2021624_41 Clupea harengus UNKNOWN 48.18703461 Plate_G NA
374 F8 2021624_29 Clupea harengus UNKNOWN 37.84211349 Plate_G NA
375 H8 2021624_6 Clupea harengus UNKNOWN 38.0619812 Plate_G NA
376 A9 2021624_33 Clupea harengus UNKNOWN Undetermined Plate_G NA
377 B9 2021624_17 Clupea harengus UNKNOWN Undetermined Plate_G NA
378 C9 2021624_28 Clupea harengus UNKNOWN Undetermined Plate_G NA
379 D9 2021624_38 Clupea harengus UNKNOWN 39.81788254 Plate_G NA
380 E9 2021624_3 Clupea harengus UNKNOWN 38.02515411 Plate_G NA
381 F9 2021624_20 Clupea harengus UNKNOWN 39.84552002 Plate_G NA
382 G9 2021624_19 Clupea harengus UNKNOWN 36.2765274 Plate_G NA
383 H9 2021624_36 Clupea harengus UNKNOWN 47.17802429 Plate_G NA
384 A10 2021624_33 Clupea harengus UNKNOWN Undetermined Plate_G NA
385 B10 2021624_17 Clupea harengus UNKNOWN Undetermined Plate_G NA
386 C10 2021624_28 Clupea harengus UNKNOWN Undetermined Plate_G NA
387 D10 2021624_38 Clupea harengus UNKNOWN 46.39860535 Plate_G NA
388 E10 2021624_3 Clupea harengus UNKNOWN 38.14785385 Plate_G NA
389 F10 2021624_20 Clupea harengus UNKNOWN Undetermined Plate_G NA
390 G10 2021624_19 Clupea harengus UNKNOWN 34.93868637 Plate_G NA
391 H10 2021624_36 Clupea harengus UNKNOWN Undetermined Plate_G NA
392 A11 2021624_21 Clupea harengus UNKNOWN 36.70544052 Plate_G NA
393 B11 2021624_31 Clupea harengus UNKNOWN 40.76830673 Plate_G NA
394 D11 2021624_9 Clupea harengus UNKNOWN 38.63124847 Plate_G NA
395 E11 2021624_39 Clupea harengus UNKNOWN 40.27198792 Plate_G NA
396 F11 Std-CH7 Clupea harengus STANDARD 37.97735214 Plate_G 1e+00
397 G11 Std-CH2 Clupea harengus STANDARD 23.85812569 Plate_G 1e+05
398 A12 2021624_21 Clupea harengus UNKNOWN 36.84037781 Plate_G NA
399 B12 2021624_31 Clupea harengus UNKNOWN Undetermined Plate_G NA
400 D12 2021624_9 Clupea harengus UNKNOWN 37.89494324 Plate_G NA
401 E12 2021624_39 Clupea harengus UNKNOWN 40.31898499 Plate_G NA
402 F12 Std-CH7 Clupea harengus STANDARD 38.828022 Plate_G 1e+00
403 G12 Std-CH2 Clupea harengus STANDARD 24.03194427 Plate_G 1e+05metabarcoding# A tibble: 10 × 93
Species sp_idx ini_conc Mock_1 Mock_2 Mock_3 Mock_4 Mock_5 Mock_6 `2019629_11` `2019629_15` `2019629_16` `2019629_22` `2019629_28` `2019629_31` `2019629_32` `2019629_6` `2019629_7` `2020620_03` `2020620_04` `2020620_05` `2020620_06` `2020620_07` `2020620_08` `2020620_11` `2020620_12` `2020620_13` `2020620_14` `2020620_15` `2020620_16` `2020620_19` `2020620_20` `2020620_21` `2020620_22` `2020620_23` `2020620_24` `2020620_27` `2020620_28` `2020620_29` `2020620_30` `2020620_31` `2020620_32` `2021624_10` `2021624_11` `2021624_14` `2021624_15` `2021624_16` `2021624_17` `2021624_18` `2021624_19` `2021624_20` `2021624_21` `2021624_22` `2021624_25` `2021624_26` `2021624_27` `2021624_28` `2021624_29` `2021624_3` `2021624_30` `2021624_31` `2021624_32` `2021624_33` `2021624_36` `2021624_37` `2021624_38` `2021624_39` `2021624_4` `2021624_40` `2021624_41` `2021624_42` `2021624_43` `2021624_44` `2021624_5` `2021624_6` `2021624_7` `2021624_8` `2021624_9` `2019629_12` `2019629_13` `2019629_14` `2019629_19` `2019629_20` `2019629_21` `2019629_23` `2019629_24` `2019629_27` `2019629_29` `2019629_3` `2019629_30` `2019629_4` `2019629_5` `2019629_8`
<chr> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int>
1 Brosme brosme 1 6022 26537 26282 55800 37606 34698 82587 0 0 0 0 0 2 0 0 6 2 1782 0 2 0 0 0 2 0 2 0 0 2 0 0 2 0 0 0 0 0 2 0 0 0 0 10 2 0 6 0 0 2 0 0 2 0 2 2 4 0 10 0 4 0 2 0 0 0 0 0 0 6 0 0 0 0 0 2 2 0 0 1 0 0 0 7 2 0 0 2 0 0 1 0
2 Cyclopterus lumpus 2 12061 63611 38494 80634 58797 37921 95245 2 0 0 2 0 0 0 0 0 4 2 0 2 4 0 0 0 6 0 8 0 0 0 0 4 0 0 0 0 2 4 0 0 2 4 0 0 0 2 0 0 0 2 0 12 4 0 10 0 4 22 4 30 2 2 10 2 6444 0 2 0 1114 0 0 0 0 2 8 2 0 3 6 1 3 0 12 1 1 1 18 90138 2 0 4
3 Hippoglossoides platessoides 3 6812 103953 53527 96043 83638 50442 118507 8214 0 0 6890 2 0 2 13672 4 17624 20868 0 5686 10148 6574 350 0 6 22342 4 7552 24912 0 12842 17432 4 10 9522 34610 10024 27240 22970 10798 28 6 16172 0 0 8272 8308 8 13990 8 4340 244510 360158 113176 477728 233486 25768 510300 240732 543826 63728 85020 3722 20754 40130 3822 4332 15434 99374 30014 23738 0 1580 1512 5490 13680 1 10716 67511 20325 1203 1 13598 2 7871 18 21045 14509 9 6 3
4 Leptoclinus maculatus 4 3725 228228 124488 237519 194652 107854 256737 160 0 0 6800 0 0 0 5240 0 4 848 0 3274 746 0 0 0 0 0 2 0 0 0 0 254 0 0 0 0 0 3020 5034 0 2 2 2 0 0 0 0 0 0 2 0 1336 0 0 5584 2 2046 0 66 1024 0 2312 18044 2 1430 0 582 0 724 0 0 0 294 3372 2 0 1 5 21640 5 4 2 218 2 1 2 2016 22234 5348 4 0
5 Mallotus villosus 5 9816 72751 35851 94465 58157 31141 90112 70304 3100 6 4 10 0 10 1372 6580 242 2040 4 256 0 0 210 5816 436 15670 10472 2 780 4 4 26074 4454 15910 1640 7958 3552 20624 6072 2 3432 4750 26782 1502 496 4 2 14 4004 14 4 48540 10376 239346 39828 12914 12 9548 15520 98442 16534 6886 3704 6 2534 12 4 10 12658 8 6 4 7354 5094 74 3270 5 11 13 3 10 0 11 73 2 6 9830 3047 40385 860 226
6 Maurolicus muelleri 6 7087 99815 29082 130790 120742 58762 162580 0 0 0 0 2 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 4 0 0 0 0 1 3 0 0 3 0 0 0 1 0 0 3 1
7 Myoxocephalus scorpius 7 8908 75120 44139 77521 70449 48500 91900 0 0 0 2 0 0 0 0 0 6 4 0 0 2 10 0 2 2 0 2 0 2 0 0 4 0 0 2 0 0 0 2 2 2 0 4 0 2 0 0 0 2 0 0 4 2 0 2 6 2 14 4 10 0 0 2 0 4 2 2 0 18 0 0 0 0 0 2 0 0 1 2 0 0 0 2 0 0 1 6 3 2 0 0
8 Pholis gunnellus 8 4477 66110 36235 58501 52223 38270 75811 100 694 0 2936 2 834 0 9916 0 2446 3070 4 3306 5562 1146 0 0 2218 4 5542 3176 0 0 4 556 0 0 2428 0 9314 1448 2034 4 824 6954 14 2866 0 1702 0 2 0 2 0 1194 14 6 3068 574 2410 16 1388 2508 4 1094 8266 5300 4572 0 734 0 2678 0 0 2 830 1420 7630 1884 0 0 1 0 0 0 0 0 0 1 12 3 1 0 0
9 Pleuronectes platessa 9 2637 41550 19983 44716 44234 27283 63749 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
10 Zz_Gadus morhua 10 5942 72763 56460 111345 82212 52685 112193 8514 8 1752 4462 5630 4822 26164 78346 50714 50744 17520 2622 32848 44932 2036 272 22108 0 25250 2 0 25320 16498 1482 12430 20104 7386 3100 12350 0 14652 11836 4 22106 5912 70490 4274 8420 17494 8180 8 25790 12904 14 30104 23940 13508 65144 11634 17790 88546 15530 49048 6 32758 694 186 18264 8326 18766 4664 79992 4 5492 1652 17274 8860 4160 48536 3 6 23677 0 5 0 11638 4592 7772 36686 18466 20476 29841 8 20.3 Run Model 1
Here we make use of the standard concentration to learn the parameters that link the known DNA concentration with observed Ct values (Y) and positive / negative qPCR amplification (Z)
\[ \begin{aligned} &\textbf{qPCR probability of detection model}\\ Z_{ij} &\sim \text{Bernoulli}(\theta_{i}) && \text{(1.1)} \\ \theta_{i} &= 1 - exp(-W_{i} \cdot \phi) && \text{(1.2)} \\ &\text{}\\ &\textbf{qPCR continuous model}\\ Y_{ij} &\sim \text{Normal}(\mu_{i}, \sigma_{i}) && \text{(2.1)} \\ \mu_{i} &= \beta0_{p} + \beta1 \cdot ln(C_{i}) && \text{(2.2)} \\ \sigma_{i} &= e^{(\gamma0 + \gamma1 \cdot ln(C_{i}))} && \text{(2.3)} \end{aligned} \]
M1 <- load_model('M1')# Prepare the data for going into the model
stan_data_M1 <- prep_stan_M1(
qpcr_data = cod_qpcr %>% filter(Sample_type=="STANDARD"),
Ct = "Ct",
standard_concentration = "Std_concentration",
plate_index = 'Plate')Plate index matches the total number of plates# Run the model
M1_output <- Run_Model(stan_object = M1, stan_data = stan_data_M1)0.4 Plot outputs of Model 1
extract_qpcr_param(M1_output) %>% as.tibble()Warning: `as.tibble()` was deprecated in tibble 2.0.0.
ℹ Please use `as_tibble()` instead.
ℹ The signature and semantics have changed, see `?as_tibble`.# A tibble: 9 × 11
parameter mean se_mean sd `2.5%` `25%` `50%` `75%` `97.5%` n_eff Rhat
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 logit_phi 3.25 0.0105 0.917 1.55 2.61 3.22 3.86 5.13 7596. 1.00
2 beta_0[Plate_B] 40.4 0.00292 0.148 40.1 40.3 40.4 40.5 40.7 2566. 1.00
3 beta_0[Plate_D] 40.6 0.00297 0.154 40.3 40.5 40.6 40.7 40.9 2688. 1.00
4 beta_0[Plate_E] 40.6 0.00295 0.154 40.3 40.5 40.6 40.7 40.9 2736. 1.00
5 beta_0[Plate_F] 40.8 0.00289 0.149 40.5 40.7 40.8 40.9 41.1 2674. 1.00
6 beta_0[Plate_G] 40.5 0.00281 0.148 40.2 40.4 40.5 40.6 40.8 2762. 1.00
7 beta_1 -1.42 0.000225 0.0111 -1.44 -1.43 -1.42 -1.41 -1.40 2430. 1.00
8 gamma_0 0.778 0.00109 0.0896 0.599 0.718 0.778 0.838 0.954 6793. 1.00
9 gamma_1 -0.233 0.000174 0.0133 -0.259 -0.242 -0.233 -0.224 -0.206 5817. 1.00plot_qpcr_prob_det(M1_output)
plot_qpcr_cont_mod(M1_output)
plot_qpcr_curves(M1_output)
plot_qpcr_cont_mod_plate_specific(M1_output)
0.5 Run Model 2
M2 <- load_model('M2')# Prepare the data for going into the model
stan_data_M2 <- prep_stan_M2(
qpcr_data = cod_qpcr,
sample_type = "Sample_type",
Ct = "Ct",
sample_name_column = "Sample_name",
standard_concentration = "Std_concentration",
plate_index = 'Plate')Plate index matches the total number of plates# Run the model
M2_output <- Run_Model(stan_object = M2, stan_data = stan_data_M2)0.6 Plot outputs of Model 2
extract_qpcr_param(M2_output) %>% as_tibble()# A tibble: 9 × 11
parameter mean se_mean sd `2.5%` `25%` `50%` `75%` `97.5%` n_eff Rhat
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 logit_phi 2.96 0.00766 0.934 1.27 2.29 2.91 3.58 4.88 14839. 1.00
2 beta_0[Plate_B] 40.4 0.00192 0.124 40.2 40.3 40.4 40.5 40.7 4202. 1.00
3 beta_0[Plate_D] 40.6 0.00197 0.130 40.4 40.5 40.6 40.7 40.9 4372. 1.00
4 beta_0[Plate_E] 40.6 0.00196 0.130 40.4 40.5 40.6 40.7 40.9 4418. 1.00
5 beta_0[Plate_F] 40.7 0.00195 0.126 40.5 40.7 40.7 40.8 41.0 4204. 1.00
6 beta_0[Plate_G] 40.5 0.00194 0.124 40.2 40.4 40.5 40.5 40.7 4105. 1.00
7 beta_1 -1.42 0.000147 0.00923 -1.44 -1.43 -1.42 -1.41 -1.40 3925. 1.00
8 gamma_0 0.686 0.000489 0.0565 0.576 0.648 0.685 0.723 0.799 13360. 1.00
9 gamma_1 -0.227 0.000115 0.0122 -0.250 -0.236 -0.228 -0.219 -0.203 11171. 1.00extract_est_conc(M2_output) %>% as_tibble()# A tibble: 84 × 5
sample_index Sample_name C_est_log `C_est_log_2.5%CI` `C_est_log_97.5%CI`
<dbl> <chr> <dbl> <dbl> <dbl>
1 1 2019629_11 -0.198 -1.51 0.821
2 2 2019629_12 -0.733 -2.78 0.666
3 3 2019629_13 1.36 0.304 2.24
4 4 2019629_14 -3.36 -7.46 -0.656
5 5 2019629_15 -1.35 -3.33 0.0593
6 6 2019629_16 0.999 0.107 1.77
7 7 2019629_19 -0.995 -3.02 0.398
8 8 2019629_20 -3.19 -7.24 -0.437
9 9 2019629_21 -3.36 -7.41 -0.628
10 10 2019629_22 -1.02 -2.44 0.0909
# ℹ 74 more rowsplot_qpcr_curves(M2_output)
plot_qpcr_prob_det(M2_output)
plot_qpcr_cont_mod(M2_output)
plot_qpcr_cont_mod_plate_specific(M2_output)
plot_est_conc(M2_output)
0.7 Run Model 3
M3 <- load_model('M3')# Trim metabarcoding data only for mock samples
moc_dat <- metabarcoding %>% select(Species,sp_idx,ini_conc,Mock_1:Mock_6)
# # Prepare the data for going into the model
stan_data_M3 <- prep_stan_M3(
metabarcoding_data = moc_dat,
mock_sequencing_columns = c('Mock_1','Mock_2','Mock_3','Mock_4','Mock_5','Mock_6'),
mock_initial_concentration = 'ini_conc',
species_index = 'sp_idx',
species_names = 'Species',
number_of_PCR = 43,
alpha_magnitude = 0.1)
# Run the model
M3_output <- Run_Model(stan_object = M3, stan_data = stan_data_M3)0.8 Plot outputs of Model 3
extract_amp_efficiecy(M3_output) Species sp_idx alpha alpha_2.5%_CI alpha_97.5%_CI
1 Brosme brosme 1 -0.014625579 -0.014736350 -0.014515151
2 Cyclopterus lumpus 2 -0.022590595 -0.022692433 -0.022491628
3 Hippoglossoides platessoides 3 -0.002313743 -0.002405521 -0.002220404
4 Leptoclinus maculatus 4 0.030800660 0.030720600 0.030880518
5 Mallotus villosus 5 -0.017323146 -0.017422432 -0.017223673
6 Maurolicus muelleri 6 0.000791568 0.000702617 0.000880306
7 Myoxocephalus scorpius 7 -0.013584814 -0.013681136 -0.013488863
8 Pholis gunnellus 8 -0.002699755 -0.002802097 -0.002595820
9 Pleuronectes platessa 9 0.002552140 0.002437823 0.002667062
10 Zz_Gadus morhua 10 0.000000000 0.000000000 0.000000000amp_eff_output_extract(M3_output) Species Pre-PCR Post-PCR ALR Post-PCR_est Post-PCR_est_2.5%_CI Post-PCR_est_97.5%_CI
1 Brosme brosme 0.08923200 0.05556938 0.01337365 0.05556887 0.05550456 0.05563241
2 Cyclopterus lumpus 0.17871590 0.07901771 0.70793133 0.07901874 0.07895763 0.07907012
3 Hippoglossoides platessoides 0.10093796 0.10672923 0.13663999 0.10672958 0.10669318 0.10677313
4 Leptoclinus maculatus 0.05519582 0.24240363 -0.46697893 0.24240231 0.24244176 0.24236069
5 Mallotus villosus 0.14545023 0.08065732 0.50196793 0.08065832 0.08060478 0.08071252
6 Maurolicus muelleri 0.10501282 0.12690236 0.17621634 0.12690047 0.12687261 0.12692714
7 Myoxocephalus scorpius 0.13199579 0.08596141 0.40490397 0.08596208 0.08591597 0.08600682
8 Pholis gunnellus 0.06633870 0.06898988 -0.28309260 0.06899039 0.06893554 0.06905000
9 Pleuronectes platessa 0.03907419 0.05093104 -0.81240387 0.05093180 0.05086511 0.05099989
10 Zz_Gadus morhua 0.08804659 0.10283804 0.00000000 0.10283742 0.10320885 0.10246730plot_amp_eff(M3_output)
0.9 Run Model 4
M4 <- load_model('M4')# Get column names for mock samples and environmental samples
mock_columns <- metabarcoding %>% select(Mock_1:Mock_6) %>% names()
sample_columns <- metabarcoding %>% select(-all_of(mock_columns),-Species,-sp_idx,-ini_conc) %>% names()
# Prepare the data for going into the model
stan_data_M4 <- prep_stan_M4(
metabarcoding_data = metabarcoding,
mock_sequencing_columns = mock_columns,
sample_sequencing_columns = sample_columns,
mock_initial_concentration = 'ini_conc',
species_index = 'sp_idx',
species_names = 'Species',
number_of_PCR = 43,
alpha_magnitude = 0.1)Warning: Using an external vector in selections was deprecated in tidyselect 1.1.0.
ℹ Please use `all_of()` or `any_of()` instead.
# Was:
data %>% select(mock_columns)
# Now:
data %>% select(all_of(mock_columns))
See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.M4_output <- Run_Model(stan_object = M4, stan_data = stan_data_M4)Warning: There were 1 divergent transitions after warmup. See
https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them.Warning: Examine the pairs() plot to diagnose sampling problems0.10 Plot outputs of Model 4
extract_amp_efficiecy(M4_output) Species sp_idx alpha alpha_2.5%_CI alpha_97.5%_CI
1 Brosme brosme 1 -0.014637120 -0.014746809 -0.014527068
2 Cyclopterus lumpus 2 -0.022601333 -0.022700178 -0.022502925
3 Hippoglossoides platessoides 3 -0.002323579 -0.002414593 -0.002231966
4 Leptoclinus maculatus 4 0.030790899 0.030712040 0.030869404
5 Mallotus villosus 5 -0.017332823 -0.017431290 -0.017233592
6 Maurolicus muelleri 6 0.000781350 0.000693773 0.000869730
7 Myoxocephalus scorpius 7 -0.013595913 -0.013691998 -0.013499636
8 Pholis gunnellus 8 -0.002710302 -0.002812885 -0.002607891
9 Pleuronectes platessa 9 0.002539397 0.002426231 0.002653054
10 Zz_Gadus morhua 10 0.000000000 0.000000000 0.000000000amp_eff_output_extract(M4_output) Species Pre-PCR Post-PCR ALR Post-PCR_est Post-PCR_est_2.5%_CI Post-PCR_est_97.5%_CI
1 Brosme brosme 0.08923200 0.05556938 0.01337365 0.05556354 0.05549950 0.05562806
2 Cyclopterus lumpus 0.17871590 0.07901771 0.70793133 0.07901390 0.07895964 0.07906605
3 Hippoglossoides platessoides 0.10093796 0.10672923 0.13663999 0.10672718 0.10668981 0.10676643
4 Leptoclinus maculatus 0.05519582 0.24240363 -0.46697893 0.24239765 0.24243944 0.24235013
5 Mallotus villosus 0.14545023 0.08065732 0.50196793 0.08065706 0.08060298 0.08071315
6 Maurolicus muelleri 0.10501282 0.12690236 0.17621634 0.12689554 0.12686985 0.12692455
7 Myoxocephalus scorpius 0.13199579 0.08596141 0.40490397 0.08595548 0.08590665 0.08600433
8 Pholis gunnellus 0.06633870 0.06898988 -0.28309260 0.06898673 0.06892828 0.06904415
9 Pleuronectes platessa 0.03907419 0.05093104 -0.81240387 0.05092429 0.05085799 0.05099132
10 Zz_Gadus morhua 0.08804659 0.10283804 0.00000000 0.10287862 0.10324586 0.10251182plot_amp_eff(M4_output)
extract_ini_prop(M4_output) Species 2019629_11 2019629_12 2019629_13 2019629_14 2019629_15 2019629_16 2019629_19 2019629_20 2019629_21 2019629_22 2019629_23 2019629_24 2019629_27 2019629_28 2019629_29 2019629_3 2019629_30 2019629_31 2019629_32 2019629_4 2019629_5 2019629_6 2019629_7 2019629_8 2020620_03 2020620_04 2020620_05 2020620_06 2020620_07 2020620_08 2020620_11 2020620_12 2020620_13 2020620_14 2020620_15 2020620_16 2020620_19 2020620_20 2020620_21 2020620_22 2020620_23 2020620_24 2020620_27 2020620_28 2020620_29 2020620_30 2020620_31 2020620_32 2021624_10 2021624_11 2021624_14 2021624_15 2021624_16 2021624_17 2021624_18 2021624_19 2021624_20 2021624_21 2021624_22 2021624_25 2021624_26 2021624_27 2021624_28 2021624_29 2021624_3 2021624_30 2021624_31 2021624_32 2021624_33 2021624_36 2021624_37 2021624_38 2021624_39 2021624_4 2021624_40 2021624_41 2021624_42 2021624_43 2021624_44 2021624_5 2021624_6 2021624_7 2021624_8 2021624_9
1 Brosme brosme 1.426889e-06 0.002113711 3.317901e-06 1.694771e-05 5.770473e-06 9.688695e-05 4.152912e-07 2.738971e-05 0.0009700373 1.193725e-05 4.761108e-04 7.254712e-04 1.383623e-05 3.962764e-05 8.049728e-06 5.513443e-05 8.932468e-07 5.954420e-04 1.053607e-05 2.413209e-06 6.687260e-04 2.968365e-06 1.690147e-04 4.628143e-05 4.885828e-05 6.441580e-02 7.235638e-05 8.060099e-05 4.824106e-06 1.699480e-05 1.073396e-04 1.025042e-04 3.493296e-06 4.298751e-05 9.520752e-07 6.773327e-07 6.498709e-05 1.534423e-05 1.051110e-05 3.987335e-05 9.112636e-06 5.727220e-06 1.012094e-05 3.687313e-06 4.637320e-07 3.841091e-05 4.556444e-06 2.756904e-06 8.988617e-06 9.663661e-06 1.272318e-04 3.210450e-04 2.355435e-05 3.820250e-04 1.319960e-05 0.0009427114 7.104207e-05 1.955959e-05 1.075170e-05 8.743218e-06 6.309795e-07 5.407519e-06 5.280063e-06 2.393705e-05 5.244043e-06 2.752042e-05 7.759601e-07 8.447352e-06 3.665868e-07 2.507540e-05 5.455720e-06 3.670489e-06 2.906858e-06 1.809327e-05 1.067551e-05 9.594516e-06 4.952411e-05 9.211967e-07 7.038276e-06 1.080336e-04 7.339950e-06 1.016430e-05 1.783096e-04 4.934030e-05
2 Cyclopterus lumpus 2.903942e-05 0.002677227 5.600354e-04 1.472016e-04 7.495553e-06 1.339838e-04 5.983917e-05 4.847117e-03 0.0010094806 2.782961e-04 1.156639e-03 4.754898e-04 1.451668e-04 5.090406e-05 6.869660e-05 7.431310e-04 8.298411e-01 5.013693e-05 1.393928e-05 4.250852e-05 3.031220e-05 4.013827e-06 6.141984e-06 1.851777e-02 1.378530e-04 9.486608e-05 9.431014e-05 1.119834e-04 1.631224e-04 2.249953e-05 1.458999e-04 1.048849e-05 4.125236e-03 4.410251e-06 6.939588e-04 8.037352e-07 6.633613e-06 2.013061e-05 1.392817e-05 1.146554e-04 1.165842e-05 7.435873e-06 1.286328e-05 4.683611e-06 1.298536e-04 1.107629e-04 6.049127e-06 3.194166e-06 1.641744e-04 4.184251e-04 3.031376e-06 2.634606e-05 3.207168e-05 1.717999e-04 1.774627e-05 0.0012058067 7.456903e-06 3.755833e-04 1.367663e-05 7.729415e-05 2.269159e-05 5.396806e-07 3.809293e-05 1.092640e-06 2.026888e-04 8.566524e-05 3.187574e-05 9.130391e-05 3.877294e-05 3.490098e-05 9.524449e-04 1.521779e-04 1.881493e-01 2.401451e-05 1.992938e-04 1.304953e-05 1.321724e-02 1.188428e-06 8.922093e-06 1.351855e-04 9.831386e-06 2.001105e-04 1.074816e-03 6.911270e-05
3 Hippoglossoides platessoides 5.471239e-02 0.056959087 9.969524e-01 7.167597e-01 4.133041e-06 6.616685e-05 9.995498e-01 9.769082e-01 0.5476545245 4.427620e-01 5.608575e-01 4.262956e-04 5.279673e-01 3.618427e-04 5.351783e-04 3.688961e-01 5.584783e-02 2.236891e-05 8.119189e-05 8.369080e-05 3.330452e-03 1.387685e-01 6.656507e-05 5.593128e-03 2.649725e-01 4.442928e-01 4.564394e-05 1.419598e-01 1.791087e-01 6.851404e-01 3.520950e-01 4.955871e-06 1.744021e-03 2.976176e-01 1.356707e-04 7.002841e-01 5.051381e-01 9.642936e-06 9.048957e-01 2.205627e-01 1.445320e-04 2.643200e-04 5.312955e-01 5.677956e-01 3.815193e-01 3.320446e-01 4.732443e-01 9.989168e-01 1.013513e-03 2.706881e-04 1.233761e-01 1.309188e-05 1.534003e-05 3.199689e-01 5.287751e-01 0.1847042298 3.111394e-01 6.657458e-04 9.958816e-01 6.682836e-01 8.967378e-01 1.945364e-01 7.741421e-01 8.672167e-01 5.746299e-01 8.382974e-01 8.422621e-01 6.982833e-01 6.689806e-01 6.566974e-01 1.538740e-01 7.884418e-01 4.900233e-01 3.358016e-01 1.950128e-01 7.845881e-01 4.931946e-01 9.994414e-01 8.266389e-01 6.793822e-05 4.913481e-02 7.029818e-02 3.196690e-01 2.080354e-01
4 Leptoclinus maculatus 2.560678e-04 0.014998576 1.025760e-04 5.531671e-02 1.490575e-06 2.041827e-05 5.272736e-05 6.975362e-04 0.4426909542 1.051977e-01 2.163390e-03 1.071828e-04 1.570263e-05 7.243768e-06 1.429367e-05 8.505102e-03 2.060535e-02 7.113225e-06 1.969096e-06 1.222611e-02 5.236826e-04 1.280347e-02 8.816593e-07 1.337429e-05 1.424562e-05 4.344845e-03 1.412986e-05 1.967993e-02 3.169661e-03 3.382800e-06 2.297632e-05 1.508575e-06 1.064882e-06 5.858240e-07 1.495699e-05 2.219721e-07 9.572339e-07 2.902179e-06 2.131298e-06 7.720183e-04 1.670238e-06 1.060840e-06 1.957922e-06 7.036611e-07 1.476382e-07 8.862107e-03 2.497237e-02 7.458136e-07 1.723635e-05 2.137171e-05 3.653709e-06 3.814636e-06 4.616996e-06 1.675191e-06 2.515690e-06 0.0002335800 9.911517e-07 3.986867e-05 2.751467e-06 8.788229e-04 1.158558e-07 7.303106e-08 2.178082e-03 1.722039e-06 1.098519e-02 8.945112e-08 5.542672e-05 3.163381e-04 9.524958e-08 4.298121e-03 1.796386e-01 1.604645e-05 4.202650e-03 3.466166e-06 6.304498e-03 1.841628e-06 8.648470e-04 2.595089e-07 1.278538e-06 2.088557e-05 2.198964e-03 3.775453e-02 2.684358e-05 7.849908e-07
5 Mallotus villosus 8.930250e-01 0.788837927 1.856243e-03 2.587181e-04 8.926558e-01 6.806936e-03 2.237945e-04 1.460124e-02 0.0009925880 4.626004e-04 8.458492e-04 3.217093e-02 2.344923e-04 3.620088e-03 3.349086e-04 3.285355e-01 2.236468e-02 3.972634e-05 7.885776e-04 7.312263e-01 9.903868e-01 2.654893e-02 2.146380e-01 9.722882e-01 6.922982e-03 8.279297e-02 3.021526e-03 1.216584e-02 5.213320e-06 1.935690e-05 4.023462e-01 3.565776e-01 2.672050e-01 3.979506e-01 7.791333e-01 2.506468e-04 3.014915e-02 4.861543e-04 5.007671e-04 6.289930e-01 3.182055e-01 8.193021e-01 1.744181e-01 2.488897e-01 2.577868e-01 4.793595e-01 2.385125e-01 2.707569e-04 2.386398e-01 4.214140e-01 3.896551e-01 2.967825e-01 1.103051e-01 2.819491e-04 2.235895e-04 0.6319873990 1.697472e-01 2.240355e-03 1.548694e-03 2.529644e-01 4.926361e-02 7.844424e-01 1.230541e-01 9.145337e-02 5.013731e-04 2.990709e-02 1.035308e-01 2.410179e-01 3.308923e-01 1.013985e-01 2.920172e-01 4.071740e-04 5.899343e-02 1.965745e-03 3.275107e-04 9.423707e-04 1.197772e-01 4.734634e-04 3.803564e-04 4.702818e-03 4.362235e-01 4.516364e-01 8.172469e-03 9.480280e-02
6 Maurolicus muelleri 7.956116e-07 0.001446523 2.199219e-06 9.026786e-06 3.854556e-06 5.793288e-05 1.045628e-04 1.649920e-05 0.0007895078 6.922293e-06 1.036907e-04 2.555800e-05 8.025492e-06 3.194248e-04 4.440114e-06 1.468174e-05 5.291417e-07 2.156250e-05 5.874080e-06 1.402187e-06 1.355446e-03 1.630641e-06 2.935917e-05 1.195072e-03 2.578840e-05 2.855654e-06 4.218997e-05 3.723820e-06 2.646294e-06 9.678290e-06 6.453983e-05 4.368875e-06 2.465447e-06 1.868700e-06 6.356554e-07 4.551527e-07 2.835061e-06 8.592145e-06 6.644633e-06 1.667426e-06 5.117987e-06 3.022432e-06 5.486670e-06 2.082236e-06 3.177141e-07 2.020596e-05 2.627995e-06 1.779521e-06 6.075356e-05 5.267311e-06 1.254928e-06 1.121282e-05 1.477163e-05 4.928488e-06 7.714055e-06 0.0005801829 3.024024e-06 1.061444e-05 6.899036e-06 3.935688e-07 3.534387e-07 2.282758e-07 2.755172e-06 6.152806e-06 2.952399e-06 2.603707e-07 4.637716e-07 1.951543e-07 2.353608e-07 1.135535e-06 3.045327e-06 2.215776e-06 1.641795e-06 1.446503e-04 6.008697e-06 5.506644e-06 8.457199e-06 6.038114e-07 3.934151e-06 5.969217e-05 4.187933e-06 1.562541e-04 6.107312e-06 2.319399e-06
7 Myoxocephalus scorpius 1.334642e-06 0.002110831 9.598786e-05 3.247770e-05 5.610530e-06 8.964782e-05 4.053883e-07 2.615464e-05 0.0009295225 1.874396e-04 1.238948e-04 4.430695e-05 1.354634e-05 3.736389e-05 4.667574e-05 1.654343e-04 1.775421e-05 3.524258e-05 1.024486e-05 2.938732e-05 2.285037e-05 2.917568e-06 4.400405e-06 4.322683e-05 1.421253e-04 1.328762e-04 6.832569e-05 6.173763e-06 5.508378e-05 1.637282e-03 1.074035e-04 9.831580e-05 7.588651e-04 3.179923e-06 9.700788e-05 6.094641e-07 6.170055e-05 1.487658e-05 1.043507e-05 7.828048e-05 8.967714e-06 5.300519e-06 1.631191e-04 3.460170e-06 4.438409e-07 2.656901e-06 6.264578e-05 2.308078e-04 1.104803e-04 8.623652e-06 4.821233e-05 1.879496e-05 3.481740e-04 8.674365e-06 1.257098e-05 0.0009090415 6.793266e-05 1.802717e-05 1.065067e-05 1.705561e-05 7.666936e-06 3.761488e-07 5.051356e-06 3.495551e-05 6.831444e-05 3.686515e-05 2.178620e-05 2.048750e-05 3.706102e-07 1.917161e-06 1.182142e-04 3.551317e-06 7.578386e-05 2.637840e-04 1.378562e-04 9.431251e-06 1.432807e-04 8.836824e-07 6.362886e-06 1.051321e-04 7.046026e-06 9.737966e-06 1.730107e-04 4.008185e-06
8 Pholis gunnellus 6.742196e-04 0.001577689 2.373508e-06 1.024967e-05 1.064372e-01 6.584288e-05 3.167318e-07 1.958508e-05 0.0008148289 1.917786e-01 5.916719e-06 2.942136e-05 8.813937e-06 3.677036e-04 2.963866e-05 2.101098e-04 1.127577e-05 1.625941e-01 6.725581e-06 9.364502e-06 1.722213e-05 1.023219e-01 3.147821e-06 3.351764e-05 3.738422e-02 6.644686e-02 1.613087e-03 8.391007e-02 9.981354e-02 1.213764e-01 7.568223e-05 5.083540e-06 7.260834e-01 5.246107e-05 2.198577e-01 2.994527e-01 3.289339e-06 1.018061e-05 2.698293e-04 7.147479e-03 5.852781e-06 3.605092e-06 1.377042e-01 2.436660e-06 3.605503e-01 1.793940e-02 4.259452e-02 3.287278e-04 3.052354e-02 3.290193e-01 1.073623e-04 3.020709e-01 1.610035e-05 6.692154e-02 8.871503e-06 0.0398593823 3.519125e-06 1.646126e-04 7.522506e-06 3.316288e-03 3.483256e-05 1.014692e-05 5.054846e-03 2.166111e-03 5.465438e-02 2.651902e-05 4.936978e-03 3.273131e-03 3.792361e-05 8.589301e-03 3.474699e-01 2.046323e-01 5.676034e-02 1.201360e-05 3.359382e-02 6.456430e-06 1.351163e-02 6.783362e-07 4.600438e-06 1.207044e-03 2.623566e-02 6.715531e-02 4.516436e-01 2.913781e-02
9 Pleuronectes platessa 7.550277e-07 0.001306791 1.996447e-06 1.367716e-06 3.446784e-06 5.373024e-05 2.756766e-07 1.586329e-05 0.0007679579 6.538880e-06 4.784159e-06 2.333675e-05 7.529946e-06 2.071991e-05 4.187849e-06 2.234135e-06 4.935231e-07 1.962429e-05 5.596687e-06 1.299416e-06 1.429930e-05 1.602398e-06 2.523401e-06 2.954117e-05 2.251505e-06 2.638678e-06 3.764786e-05 3.475288e-06 2.485173e-06 9.448537e-06 6.249498e-05 4.128385e-06 2.389623e-06 1.797247e-06 6.329472e-07 4.228624e-07 2.720637e-06 8.092130e-06 6.123208e-06 1.500264e-06 4.725967e-06 3.019232e-06 5.334619e-06 1.986929e-06 3.084504e-07 1.477587e-06 2.423745e-06 1.643085e-06 4.714757e-06 4.952331e-06 1.143476e-06 1.064821e-05 1.271962e-05 4.920185e-06 6.958770e-06 0.0005792732 2.961776e-06 9.864107e-06 6.726322e-06 3.719510e-07 3.192891e-07 2.105274e-07 2.434944e-07 4.278235e-07 2.873703e-06 2.480274e-07 4.336309e-07 1.898823e-07 2.322339e-07 1.066567e-06 3.085777e-06 2.048020e-06 1.524667e-06 9.648066e-06 5.774272e-06 4.992747e-06 7.709123e-07 5.691438e-07 3.652151e-06 5.713867e-05 3.845075e-06 5.284803e-06 6.136400e-06 2.175982e-06
10 Zz_Gadus morhua 5.129894e-02 0.127971639 4.228308e-04 2.274476e-01 8.751715e-04 9.926085e-01 7.829030e-06 2.840446e-03 0.0033805982 2.593080e-01 4.342623e-01 9.659720e-01 4.715856e-01 9.951751e-01 9.989539e-01 2.928725e-01 7.131007e-02 8.366147e-01 9.990753e-01 2.563775e-01 3.650209e-03 7.195440e-01 7.850800e-01 2.239900e-03 6.903492e-01 3.374735e-01 9.949908e-01 7.420784e-01 7.176747e-01 1.917646e-01 2.449725e-01 6.431910e-01 7.409626e-05 3.043245e-01 6.522393e-05 9.300370e-06 4.645696e-01 9.994241e-01 9.428393e-02 1.422888e-01 6.816029e-01 1.804044e-01 1.563834e-01 1.832957e-01 1.205526e-05 1.616209e-01 2.205981e-01 2.428111e-04 7.294568e-01 2.488277e-01 4.866770e-01 4.007417e-01 8.892276e-01 6.122536e-01 4.709318e-01 0.1389983932 5.189564e-01 9.964558e-01 2.510685e-03 7.445303e-02 5.393198e-02 2.100420e-02 9.551946e-02 3.909554e-02 3.589471e-01 1.316184e-01 4.915936e-02 5.698871e-02 4.911444e-05 2.289526e-01 2.591808e-02 6.338997e-03 2.017892e-01 6.617569e-01 7.644017e-01 2.144186e-01 3.592325e-01 8.003164e-05 1.729449e-01 9.935361e-01 4.861748e-01 3.727740e-01 2.190497e-01 6.678963e-01bar_plot_est_ini_prop(M4_output)
heatmap_plot_est_ini_prop(M4_output)
0.11 Run Model 5
M5 <- load_model('M5')mock_columns <- metabarcoding %>% select(Mock_1:Mock_6) %>% names()
sample_columns <- metabarcoding %>% select(-all_of(mock_columns),-Species,-sp_idx,-ini_conc) %>% names()
# qpcr <- qpcr %>% filter(qpcr$Sample_name%in%sample_columns|qpcr$Sample_type=='STANDARD')
stan_data_M5 <- prep_stan_M5(
qpcr_data = cod_qpcr,
sample_type = "Sample_type",
Ct = "Ct",
sample_name_column = "Sample_name",
standard_concentration = "Std_concentration",
plate_index = 'Plate',
metabarcoding_data = metabarcoding,
mock_sequencing_columns = mock_columns,
sample_sequencing_columns = sample_columns,
mock_initial_concentration = 'ini_conc',
species_index = 'sp_idx',
species_names = 'Species',
number_of_PCR = 43,
alpha_magnitude = 0.1)
M5_output <- Run_Model(stan_object = M5, stan_data = stan_data_M5,
treedepth = 12,iterations = 2000,warmup = 1000)0.12 Plot outputs of Model 5
extract_amp_efficiecy(M5_output) Species sp_idx alpha alpha_2.5%_CI alpha_97.5%_CI
1 Brosme brosme 1 -0.014632546 -0.014743197 -0.014520084
2 Cyclopterus lumpus 2 -0.022597376 -0.022700414 -0.022495473
3 Hippoglossoides platessoides 3 -0.002318253 -0.002411883 -0.002225424
4 Leptoclinus maculatus 4 0.030795895 0.030717400 0.030876177
5 Mallotus villosus 5 -0.017328376 -0.017429810 -0.017225877
6 Maurolicus muelleri 6 0.000785499 0.000695353 0.000875927
7 Myoxocephalus scorpius 7 -0.013592639 -0.013689874 -0.013496474
8 Pholis gunnellus 8 -0.002706073 -0.002811375 -0.002599341
9 Pleuronectes platessa 9 0.002543134 0.002425491 0.002659690
10 Zz_Gadus morhua 10 0.000000000 0.000000000 0.000000000amp_eff_output_extract(M5_output) Species Pre-PCR Post-PCR ALR Post-PCR_est Post-PCR_est_2.5%_CI Post-PCR_est_97.5%_CI
1 Brosme brosme 0.08923200 0.05556938 0.01337365 0.05556493 0.05550254 0.05563059
2 Cyclopterus lumpus 0.17871590 0.07901771 0.70793133 0.07901377 0.07895090 0.07907124
3 Hippoglossoides platessoides 0.10093796 0.10672923 0.13663999 0.10673329 0.10669151 0.10676925
4 Leptoclinus maculatus 0.05519582 0.24240363 -0.46697893 0.24240808 0.24247094 0.24235894
5 Mallotus villosus 0.14545023 0.08065732 0.50196793 0.08065863 0.08060000 0.08071936
6 Maurolicus muelleri 0.10501282 0.12690236 0.17621634 0.12689638 0.12686571 0.12692602
7 Myoxocephalus scorpius 0.13199579 0.08596141 0.40490397 0.08595282 0.08590585 0.08599411
8 Pholis gunnellus 0.06633870 0.06898988 -0.28309260 0.06898743 0.06892582 0.06905194
9 Pleuronectes platessa 0.03907419 0.05093104 -0.81240387 0.05092372 0.05085126 0.05099288
10 Zz_Gadus morhua 0.08804659 0.10283804 0.00000000 0.10286095 0.10323548 0.10248569plot_amp_eff(M5_output)
extract_ini_prop(M5_output) Species 2019629_11 2019629_12 2019629_13 2019629_14 2019629_15 2019629_16 2019629_19 2019629_20 2019629_21 2019629_22 2019629_23 2019629_24 2019629_27 2019629_28 2019629_29 2019629_3 2019629_30 2019629_31 2019629_32 2019629_4 2019629_5 2019629_6 2019629_7 2019629_8 2020620_03 2020620_04 2020620_05 2020620_06 2020620_07 2020620_08 2020620_11 2020620_12 2020620_13 2020620_14 2020620_15 2020620_16 2020620_19 2020620_20 2020620_21 2020620_22 2020620_23 2020620_24 2020620_27 2020620_28 2020620_29 2020620_30 2020620_31 2020620_32 2021624_10 2021624_11 2021624_14 2021624_15 2021624_16 2021624_17 2021624_18 2021624_19 2021624_20 2021624_21 2021624_22 2021624_25 2021624_26 2021624_27 2021624_28 2021624_29 2021624_3 2021624_30 2021624_31 2021624_32 2021624_33 2021624_36 2021624_37 2021624_38 2021624_39 2021624_4 2021624_40 2021624_41 2021624_42 2021624_43 2021624_44 2021624_5 2021624_6 2021624_7 2021624_8 2021624_9
1 Brosme brosme 9.231328e-07 0.0011427398 1.109676e-06 1.914366e-05 3.713895e-06 0.0010544566 3.897425e-07 2.211078e-05 0.0008740736 1.048687e-05 7.976465e-04 0.0046725932 1.609239e-05 1.976386e-04 8.371236e-05 7.240862e-05 7.247218e-07 2.384857e-03 1.712053e-04 2.271091e-06 6.480539e-04 5.548855e-06 6.058870e-04 2.197117e-05 1.358643e-04 9.325875e-02 0.0006716699 2.638360e-04 9.643028e-06 1.298402e-05 7.633059e-05 2.258024e-04 2.874744e-06 5.515015e-05 1.296591e-06 8.496453e-07 1.065417e-04 1.262792e-04 7.445685e-06 4.308530e-05 1.600087e-05 4.162812e-06 6.832783e-06 2.911686e-06 7.786072e-07 4.282720e-05 4.393500e-06 1.092268e-06 1.525076e-05 4.397822e-06 2.163654e-04 4.762222e-04 8.719058e-05 7.800645e-04 1.089257e-05 2.744056e-04 1.275719e-04 0.0005200549 3.924198e-06 8.891326e-06 3.440963e-07 5.249819e-06 5.574269e-06 2.426955e-05 4.144574e-06 3.080475e-05 5.670260e-07 8.606541e-06 1.811894e-07 2.954514e-05 4.892406e-06 2.411785e-06 2.213747e-06 2.458335e-05 2.339317e-05 7.838391e-06 7.101183e-05 4.202874e-07 5.398323e-06 0.0020926588 7.377291e-06 5.833390e-06 2.129321e-04 1.346655e-04
2 Cyclopterus lumpus 2.893868e-05 0.0014526557 5.429246e-04 1.789371e-04 4.605607e-06 0.0013470430 5.905755e-05 4.820781e-03 0.0009432168 3.367035e-04 1.955146e-03 0.0028625999 2.241106e-04 2.516229e-04 9.852501e-04 9.915835e-04 8.798919e-01 1.266158e-04 2.245502e-04 5.127834e-05 2.557674e-05 7.037919e-06 1.390276e-05 1.826730e-02 3.897365e-04 1.324019e-04 0.0007958808 3.660542e-04 4.852930e-04 1.936584e-05 9.624621e-05 1.567667e-05 4.096604e-03 4.322186e-06 6.961140e-04 9.280038e-07 7.925701e-06 1.731860e-04 1.016913e-05 1.268661e-04 1.994371e-05 5.563158e-06 8.895189e-06 3.979230e-06 1.354873e-04 1.251120e-04 5.899112e-06 1.256016e-06 5.219968e-04 5.316745e-04 3.767244e-06 1.582197e-05 1.120723e-04 3.388896e-04 1.371456e-05 3.195234e-04 8.478974e-06 0.0224087600 4.569077e-06 8.135347e-05 2.343311e-05 3.188852e-07 4.107419e-05 6.919556e-07 3.001989e-04 9.657978e-05 3.260883e-05 9.652012e-05 3.731795e-05 4.172281e-05 9.666192e-04 1.485683e-04 2.313747e-01 3.056934e-05 6.662718e-04 1.035581e-05 1.930359e-02 4.599764e-07 7.177950e-06 0.0028639138 9.736121e-06 2.913288e-04 1.341647e-03 1.846913e-04
3 Hippoglossoides platessoides 5.739960e-02 0.0591106412 9.974110e-01 8.798905e-01 2.812307e-06 0.0006949681 9.995516e-01 9.779517e-01 0.5437172088 5.602985e-01 9.505813e-01 0.0027840038 9.089327e-01 2.460801e-03 8.506037e-03 4.948839e-01 5.921695e-02 6.373084e-05 2.141683e-03 1.060011e-04 3.317856e-03 4.507055e-01 2.349839e-04 5.602139e-03 7.706407e-01 6.437931e-01 0.0004254249 5.060990e-01 5.539920e-01 8.090176e-01 4.506031e-01 8.432865e-06 1.725823e-03 4.093700e-01 1.376728e-04 7.003405e-01 8.721931e-01 8.390971e-05 9.815605e-01 2.468296e-01 3.718642e-04 3.143906e-04 6.198139e-01 6.734162e-01 3.814954e-01 3.773228e-01 5.713282e-01 9.991728e-01 3.490544e-03 3.474778e-04 2.101856e-01 8.257763e-06 5.186450e-05 6.620654e-01 9.878052e-01 2.132570e-01 5.890346e-01 0.0424524344 9.983392e-01 7.135827e-01 9.463422e-01 1.984067e-01 8.388650e-01 9.003607e-01 8.853638e-01 9.509925e-01 8.817610e-01 7.391249e-01 6.690098e-01 8.146584e-01 1.558116e-01 7.923837e-01 6.026339e-01 9.546887e-01 6.843464e-01 9.724287e-01 7.199504e-01 9.995232e-01 9.730341e-01 0.0014024785 9.324476e-02 1.113475e-01 4.070425e-01 5.969492e-01
4 Leptoclinus maculatus 2.685486e-04 0.0154740240 1.001022e-04 6.789936e-02 9.822955e-07 0.0002289443 5.249389e-05 6.886773e-04 0.4466264679 1.331693e-01 3.658504e-03 0.0006814030 2.452363e-05 4.033831e-05 2.160663e-04 1.140689e-02 2.185191e-02 2.015759e-05 3.361930e-05 1.558047e-02 5.225070e-04 4.156629e-02 2.282468e-06 8.169454e-06 4.026100e-05 6.294769e-03 0.0001349348 7.017410e-02 9.804245e-03 3.035557e-06 1.833298e-05 2.558317e-06 9.884908e-07 5.906098e-07 1.538689e-05 2.760748e-07 1.107441e-06 2.690296e-05 1.805307e-06 8.645602e-04 3.006724e-06 8.881745e-07 1.422847e-06 6.014362e-07 2.278460e-07 1.007602e-02 3.013100e-02 3.713811e-07 5.593475e-05 2.546238e-05 6.118064e-06 2.825763e-06 1.899182e-05 2.706775e-06 2.317376e-06 9.245725e-05 1.422043e-06 0.0023664908 1.098926e-06 9.383983e-04 6.954009e-08 5.171119e-08 2.361161e-03 1.702827e-06 1.692223e-02 7.397476e-08 5.787380e-05 3.351190e-04 5.432879e-08 5.332693e-03 1.818751e-01 1.589282e-05 5.170384e-03 5.514966e-06 2.214343e-02 1.561257e-06 1.262514e-03 1.266512e-07 1.069423e-06 0.0005221141 4.168597e-03 5.985655e-02 3.117407e-05 1.370053e-06
5 Mallotus villosus 9.366511e-01 0.8911316536 1.838843e-03 3.148473e-04 8.931736e-01 0.1391465566 2.247379e-04 1.460120e-02 0.0010464545 5.791923e-04 1.420910e-03 0.2150665196 3.854396e-04 2.556298e-02 5.213338e-03 4.406051e-01 2.370100e-02 1.025234e-04 2.240068e-02 9.320014e-01 9.915443e-01 8.617252e-02 7.733786e-01 9.744316e-01 2.012994e-02 1.200096e-01 0.0489884680 4.340205e-02 1.014409e-05 1.673207e-05 5.146484e-01 8.216253e-01 2.674329e-01 5.474171e-01 7.790708e-01 2.564779e-04 5.206632e-02 6.045653e-03 5.308308e-04 7.038735e-01 8.372772e-01 9.814690e-01 2.033825e-01 2.953120e-01 2.577484e-01 5.448111e-01 2.880268e-01 2.560705e-04 8.262359e-01 5.593032e-01 6.637943e-01 4.907575e-01 7.349540e-01 5.770461e-04 3.731479e-04 7.379191e-01 3.214645e-01 0.1439414221 1.511717e-03 2.701287e-01 5.197986e-02 8.000600e-01 1.333571e-01 9.497190e-02 7.682887e-04 3.392738e-02 1.083929e-01 2.551112e-01 3.309079e-01 1.258429e-01 2.956117e-01 4.042128e-04 7.250264e-02 5.559912e-03 1.125566e-03 1.167851e-03 1.748785e-01 4.655028e-04 4.491832e-04 0.2731719391 8.273859e-01 7.157941e-01 1.038742e-02 2.721225e-01
6 Maurolicus muelleri 6.122922e-07 0.0008358142 7.330208e-07 1.025128e-05 2.472606e-06 0.0006193005 1.049031e-04 1.428636e-05 0.0008702222 6.232405e-06 1.689891e-04 0.0001188307 8.453381e-06 2.206719e-03 4.521407e-05 1.821761e-05 4.555005e-07 5.631234e-05 1.001120e-04 1.331799e-06 1.369336e-03 3.505193e-06 9.846532e-05 1.152894e-03 6.947972e-05 2.783688e-06 0.0004028071 7.565824e-06 5.272880e-06 8.900136e-06 5.094927e-05 6.862683e-06 2.057415e-06 1.832541e-06 8.902273e-07 6.034747e-07 3.530920e-06 7.312513e-05 5.091502e-06 1.393993e-06 9.300330e-06 2.513077e-06 4.114617e-06 1.900362e-06 5.056138e-07 2.218560e-05 2.557974e-06 7.671202e-07 1.914358e-04 2.633492e-06 1.600283e-06 7.006321e-06 5.215854e-05 7.227828e-06 6.069695e-06 1.876097e-04 3.943503e-06 0.0003191068 2.492845e-06 3.285099e-07 2.208746e-07 1.522786e-07 2.897430e-06 5.907588e-06 2.255573e-06 2.237913e-07 3.052321e-07 1.189827e-07 1.159010e-07 1.073972e-06 2.844391e-06 1.514837e-06 1.205482e-06 3.811355e-04 1.346592e-05 4.614520e-06 1.188923e-05 2.671089e-07 3.218463e-06 0.0013130313 4.200075e-06 2.345300e-04 3.691113e-06 3.831369e-06
7 Myoxocephalus scorpius 9.283214e-07 0.0011383979 7.990572e-05 3.845392e-05 3.697051e-06 0.0010061824 3.779877e-07 2.180657e-05 0.0009379749 2.338537e-04 2.030457e-04 0.0001850928 1.485474e-05 1.789333e-04 6.515749e-04 2.174598e-04 1.846659e-05 9.519271e-05 1.571258e-04 3.636810e-05 2.013991e-05 5.330622e-06 1.088567e-05 2.287011e-05 4.047770e-04 1.903277e-04 0.0006808943 1.313029e-05 1.617569e-04 1.932943e-03 7.331210e-05 2.157600e-04 7.453805e-04 3.141526e-06 9.762543e-05 8.531458e-07 1.039629e-04 1.301774e-04 8.168124e-06 8.683647e-05 1.537446e-05 4.069093e-06 1.811759e-04 3.015155e-06 7.597662e-07 2.528599e-06 7.277302e-05 2.162053e-04 3.549245e-04 4.318943e-06 8.018893e-05 1.284706e-05 2.172678e-03 1.360537e-05 1.032458e-05 2.619207e-04 1.223030e-04 0.0005459828 3.643066e-06 1.792546e-05 7.420865e-06 2.446600e-07 5.346781e-06 3.561893e-05 9.661458e-05 4.186876e-05 2.223267e-05 2.141223e-05 1.559962e-07 1.770078e-06 1.163574e-04 2.564736e-06 9.010034e-05 6.750228e-04 4.622202e-04 7.686286e-06 2.075252e-04 3.701289e-07 5.552154e-06 0.0021066871 6.980364e-06 6.349787e-06 1.964946e-04 6.126631e-06
8 Pholis gunnellus 7.073850e-04 0.0009421676 8.527532e-07 1.208836e-05 1.065450e-01 0.0006675563 2.916935e-07 1.658781e-05 0.0007387880 2.428385e-01 6.045862e-06 0.0001347253 1.057481e-05 2.489185e-03 4.299586e-04 2.791829e-04 1.172417e-05 6.970308e-01 1.066057e-04 1.127688e-05 1.481266e-05 3.324034e-01 7.523196e-06 1.673779e-05 1.086840e-01 9.625899e-02 0.0263265185 2.992975e-01 3.088218e-01 1.433820e-01 5.170567e-05 8.225250e-06 7.259374e-01 6.999709e-05 2.198156e-01 2.993823e-01 3.830081e-06 8.489872e-05 2.840381e-04 7.991522e-03 1.074359e-05 2.634048e-06 1.605791e-01 2.012087e-06 3.605791e-01 2.039522e-02 5.145762e-02 3.198137e-04 1.057358e-01 4.366714e-01 1.815301e-04 4.995610e-01 6.417296e-05 1.384807e-01 7.061197e-06 4.307048e-02 4.470847e-06 0.0096648053 2.731853e-06 3.540110e-03 3.615543e-05 1.023186e-05 5.475414e-03 2.249796e-03 8.414753e-02 2.983176e-05 5.167819e-03 3.464518e-03 3.723172e-05 1.064626e-02 3.518990e-01 2.057027e-01 6.982387e-02 1.755589e-05 1.177266e-01 4.991293e-06 1.972749e-02 2.795105e-07 3.679254e-06 0.0663468207 4.979935e-02 1.063592e-01 5.753887e-01 8.361283e-02
9 Pleuronectes platessa 5.592892e-07 0.0007931227 7.269535e-07 1.239840e-06 2.449073e-06 0.0006320063 2.740094e-07 1.298539e-05 0.0007673267 6.109238e-06 5.062898e-06 0.0001146153 8.894788e-06 1.103989e-04 4.482459e-05 2.235123e-06 3.945160e-07 5.041187e-05 9.209418e-05 1.209279e-06 1.232471e-05 3.120689e-06 6.426380e-06 1.477733e-05 4.184026e-06 2.536065e-06 0.0003309937 6.941433e-06 5.094418e-06 7.627753e-06 4.966268e-05 7.007320e-06 1.929630e-06 1.647876e-06 7.940084e-07 5.371231e-07 3.304360e-06 7.184106e-05 4.646972e-06 1.311455e-06 8.170460e-06 2.329224e-06 4.016429e-06 1.799209e-06 4.706368e-07 1.232969e-06 2.498457e-06 8.203318e-07 8.805367e-06 2.630114e-06 1.590257e-06 7.658122e-06 5.110481e-05 8.178778e-06 6.000522e-06 1.786897e-04 3.504407e-06 0.0002881557 2.516068e-06 2.978328e-07 1.887380e-07 1.274901e-07 2.046417e-07 2.791849e-07 2.368933e-06 2.125700e-07 2.918481e-07 1.048296e-07 1.151630e-07 1.051900e-06 2.829804e-06 1.446574e-06 1.234517e-06 1.378747e-05 1.325324e-05 4.542471e-06 8.231413e-07 2.452327e-07 2.875731e-06 0.0013548026 3.824152e-06 3.557493e-06 3.171432e-06 3.396778e-06
10 Zz_Gadus morhua 4.941402e-03 0.0279787833 2.384253e-05 5.163521e-02 2.607046e-04 0.8546029858 5.840354e-06 1.849858e-03 0.0034782666 6.252107e-02 4.120337e-02 0.7733796164 9.037439e-02 9.665014e-01 9.838240e-01 5.152309e-02 1.530649e-02 3.000694e-01 9.745723e-01 5.220842e-02 2.525085e-03 8.912776e-02 2.256411e-01 4.614999e-04 9.950101e-02 4.005682e-02 0.9212424079 8.036981e-02 1.267047e-01 4.559885e-02 3.433193e-02 1.778844e-01 5.403268e-05 4.307619e-02 1.638795e-04 1.666335e-05 7.551035e-02 9.931840e-01 1.758734e-02 4.018130e-02 1.622684e-01 1.819449e-02 1.601804e-02 3.125561e-02 3.889041e-05 4.720103e-02 5.896820e-02 3.079430e-05 6.338942e-02 3.106819e-03 1.255289e-01 9.150814e-03 2.624357e-01 1.977262e-01 1.176531e-02 4.438857e-03 8.922918e-02 0.7774927872 1.281439e-04 1.170133e-02 1.610092e-03 1.516909e-03 1.988624e-02 2.349137e-03 1.239257e-02 1.488053e-02 4.564483e-03 1.837523e-03 7.083642e-06 4.344449e-02 1.370895e-02 1.336935e-03 1.839975e-02 3.860325e-02 1.734794e-01 2.636190e-02 6.458629e-02 9.100200e-06 2.648770e-02 0.6488255540 2.536929e-02 6.100970e-03 5.392254e-03 4.698138e-02bar_plot_est_ini_prop(M5_output)
bar_plot_est_ini_prop(M4_output)
heatmap_plot_est_ini_prop(M5_output)
plot_est_ini_conc(M5_output)